Likely there’s something in the hardboard in the large section…voids, or thicker glue.
In the future do not pull your material from the bed until you’ve verified that the cuts come out! If you use something (the honeycomb hold down pins are perfect for this) to hold down your material you can use tweezers or tape to pull your cuts out - if some of them don’t come out, close the lid and run your cut line again (do not move your design even if it looks off!)